OK, but two issues...
If you want to leave your a/c on while your boat isn't attended, make sure of the following:(1) Is there a high-quality and *clean* filter on the raw water intake? If not, debris could clog the sea water pump's impeller. Most marine a/c systems are fitted with magnetic sea water pumps, which cannot run dry without damaging the impeller or, at the extreme, ruining the pump (replacement: $250+). In addition, damage to the a/c unit's compressor could result; however, most modern marine a/c units have automatic error-sensing controls that shut down the compressor if sea water isn't available (check your manual to find out whether your unit has this feature). (2) Have you made provisions to drain condensate? I've run into some "professional" installations (including two in previous boats of mine) in which no thought was given to the condensate that collects in the unit's drain pan. If not drained, the moisture will spill out of the drain pan and could do serious damage (dry rot) to woodwork and bulkheads. The condensate can be drained to the bilge, but I prefer to pump it overboard. You can use a shower sump pump (a plastic box containing a bilge pump and float switch) to collect the condensate to be pumped through a through-hull mounted well above the waterline. (3) Are you using insulated supply hoses? Non-insulated hoses will produce a surprising amount of condensation, which may drip into areas that aren't well ventilated (thus allowing water to collect and mildew to form). Insulated hose isn't easy to find; building supply chains (such as Lowe's or Home Depot) don't carry it. You need to go to a contractor supplier. Insulated hose is also available from marine air conditioner manufacturers as part of their pricey installation kits. A budget option (and probably just as good) would be to use drier hose and wrap it tightly and securely with hot water heater insulation (make sure it has an external vapor barrier wrap). Disclaimer - I'm not an HVAC expert; I've learned the above by installing a/c systems in three boats that I've owned. Perhaps there's an HVAC expert on the list who would like to comment???